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Yorodumi- PDB-6e8g: CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e8g | |||||||||||||||||||||||||||
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Title | CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ssDNA at 2.9 Angstrom resolution | |||||||||||||||||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / PROTEIN FIBRIL / ESCRT-III / CHMP1B / IST1 / ssDNA | |||||||||||||||||||||||||||
Function / homology | Function and homology information MIT domain binding / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / abscission / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway ...MIT domain binding / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / abscission / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / cytoskeleton-dependent cytokinesis / regulation of centrosome duplication / nuclear membrane reassembly / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / positive regulation of collateral sprouting / multivesicular body sorting pathway / membrane fission / plasma membrane repair / membrane coat / late endosome to vacuole transport / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of mitotic spindle assembly / multivesicular body assembly / Flemming body / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / positive regulation of proteolysis / autophagosome membrane / endoplasmic reticulum-Golgi intermediate compartment / autophagosome maturation / nuclear pore / multivesicular body / viral budding from plasma membrane / establishment of protein localization / kinetochore / autophagy / azurophil granule lumen / protein localization / protein transport / nuclear envelope / midbody / endosome membrane / cadherin binding / protein domain specific binding / lysosomal membrane / cell division / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / protein-containing complex binding / chromatin / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||||||||||||||
Authors | Talledge, N. / Frost, A. / McCullough, J. | |||||||||||||||||||||||||||
Funding support | United States, 8items
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Citation | Journal: Biorxiv / Year: 2018 Title: The ESCRT-III proteins IST1 and CHMP1B assemble around nucleic acids Authors: Talledge, N. / McCullough, J. / Wenzel, D.M. / Nguyen, H.C. / Lalonde, M. / Bajorek, M. / Skalicky, J.J. / Frost, A. / Sundquist, W.I. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6e8g.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6e8g.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6e8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e8g_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6e8g_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6e8g_validation.xml.gz | 276.4 KB | Display | |
Data in CIF | 6e8g_validation.cif.gz | 387 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/6e8g ftp://data.pdbj.org/pub/pdb/validation_reports/e8/6e8g | HTTPS FTP |
-Related structure data
Related structure data | 9005MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 36 / Rise per n subunits: 3.17 Å / Rotation per n subunits: 21.16 °) |
-Components
#1: Protein | Mass: 40024.711 Da / Num. of mol.: 36 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIPL / References: UniProt: P53990 #2: Protein | Mass: 22140.354 Da / Num. of mol.: 36 / Mutation: K37E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP1B, C18orf2 / Plasmid: pGEX / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q7LBR1 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Helical assembly of IST1 and CHMP1B protein bound to ssDNA Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Homo sapiens (human) / Cellular location: cytoplasm | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) RIPL | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 292.15 K / Details: 0 mm offset with 10 sec wait time and 2-4 sec blot |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Cs: 2.6 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6.2 sec. / Electron dose: 62 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2980 |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 3-32 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 21.16 ° / Axial rise/subunit: 3.17 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 224252 Details: Helical particle segments were selected using RELION manualpick and extracted using overlapping segments with an asymmetric unit of 17 subunits with a 3.0 Angstrom rise (51 Angstrom total). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101990 / Num. of class averages: 1 / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 52.5 / Protocol: AB INITIO MODEL / Space: REAL |